Filter Columns by Annotation

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2FcolumnFilterByAnnotation.html;h=1ece1cc2e6c8c4af4f2187228c0734689c7b8949;hb=25687914d19af3fc0057e9465a29d2dc6a94f27a;hp=c5f42df4c6b5f7c2fc987f3c8e48396d95a2e18b;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/calculations/columnFilterByAnnotation.html index c5f42df..1ece1cc 100644 --- a/help/html/calculations/columnFilterByAnnotation.html +++ b/help/html/calculations/columnFilterByAnnotation.html @@ -20,42 +20,39 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Filter Columns by Annotation +Select/Hide Columns by Annotation

- Filter Columns by Annotation + Select/Hide Columns by Annotation

Jalview allows the columns of an alignment to be filtered using - any annotation rows added to that alignment.

- From "Select" menu - → "Select by Annotation..." to bring - up the Select by Annotation window. The filter options vary depending +

From Jalview 2.9 columns of an alignment can be filtered using + any annotation row added to that alignment.

+ To carry out this operation, navigate to "Select→Select/Hide Columns by Annotation..." to bring + up the 'Select/Hide by Annotation' window. The filter options vary depending on the type of annotation selected. If an annotation that has a numeric values is selected, the threshold filter option is activated as seen in the - figure on the right below. + figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.
-
+
+ + + + + +

Select which annotation to base the filtering on using the - top-most selection box.
The target annotation row can be selected using the drop-down option menu in the top-most part of the window.
Search Filter
- When a text is entered in the textfield on the search - filter section, the "Display Label" and "Description" - checkboxes becomes selectable.
- On selecting any of the checkboxes, a regular expresion +
- When a text is entered in the text box within the Search + Filter section, the 'Display Label' and 'Description' + options becomes enabled for selection.
- On selecting any of the options, a regular expression search (RegEx) is executed on the specified field of the current annotation row selected, and the matching columns will be highlighted in the alignment.
- Structure Filter
  - Alignment columns can also be filtered by the type of - secondary structure present in a choosen annotation row.
  - This can be achieved by ticking the type of structure you wish to filter by under the structures filter section.
  @@ -71,7 +68,7 @@
  - This filter is only activated for annotation which contain numeric values
  - Select whether to Filter the alignment above or below an +
  - Select whether to filter the alignment above or below an adjustable threshold with the selection box within the threshold filter section.
  - Change the threshold value with the slider, or enter the @@ -79,15 +76,15 @@
- Actions
  - The "Select" and "Hide" radio buttons +
  - The 'Select' and 'Hide' radio buttons determines the action that will be carried out on the matching columns in the alignment during the filtering process.
  - The default option is "Select" and this simply +
  - The default option is 'Select' and this simply enables column selection on the matching alignment column.
  - While the "Hide" option enables the matching columns to +
  - While the 'Hide' option enables the matching columns to be hidden automatically during the filtering process.
  - The "Ok" button applies the filter when clicked.
  - And finally, The "Cancel" button restores the alignment to its previous state before the filtering when clicked. +
  - The 'Ok' button applies the filter when clicked.
  - And finally, the 'Cancel' button restores the alignment to its previous state before any filtering was applied.